51
|
Dembek M, Willing SE, Hong HA, Hosseini S, Salgado PS, Cutting SM. Inducible Expression of spo0A as a Universal Tool for Studying Sporulation in Clostridium difficile. Front Microbiol 2017; 8:1793. [PMID: 28983286 PMCID: PMC5613124 DOI: 10.3389/fmicb.2017.01793] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/05/2017] [Indexed: 01/01/2023] Open
Abstract
Clostridium difficile remains a leading nosocomial pathogen, putting considerable strain on the healthcare system. The ability to form endospores, highly resistant to environmental insults, is key to its persistence and transmission. However, important differences exist between the sporulation pathways of C. difficile and the model Gram-positive organism Bacillus subtilis. Amongst the challenges in studying sporulation in C. difficile is the relatively poor levels of sporulation and high heterogeneity in the sporulation process. To overcome these limitations we placed Ptet regulatory elements upstream of the master regulator of sporulation, spo0A, generating a new strain that can be artificially induced to sporulate by addition of anhydrotetracycline (ATc). We demonstrate that this strain is asporogenous in the absence of ATc, and that ATc can be used to drive faster and more efficient sporulation. Induction of Spo0A is titratable and this can be used in the study of the spo0A regulon both in vitro and in vivo, as demonstrated using a mouse model of C. difficile infection (CDI). Insights into differences between the sporulation pathways in B. subtilis and C. difficile gained by study of the inducible strain are discussed, further highlighting the universal interest of this tool. The Ptet-spo0A strain provides a useful background in which to generate mutations in genes involved in sporulation, therefore providing an exciting new tool to unravel key aspects of sporulation in C. difficile.
Collapse
Affiliation(s)
- Marcin Dembek
- Institute for Cell and Molecular Biosciences, Newcastle UniversityNewcastle upon Tyne, United Kingdom
| | - Stephanie E Willing
- School of Biological Sciences, Royal Holloway, University of LondonLondon, United Kingdom
| | - Huynh A Hong
- School of Biological Sciences, Royal Holloway, University of LondonLondon, United Kingdom
| | - Siamand Hosseini
- School of Biological Sciences, Royal Holloway, University of LondonLondon, United Kingdom
| | - Paula S Salgado
- Institute for Cell and Molecular Biosciences, Newcastle UniversityNewcastle upon Tyne, United Kingdom
| | - Simon M Cutting
- School of Biological Sciences, Royal Holloway, University of LondonLondon, United Kingdom
| |
Collapse
|
52
|
|
53
|
Borton MA, Sabag-Daigle A, Wu J, Solden LM, O’Banion BS, Daly RA, Wolfe RA, Gonzalez JF, Wysocki VH, Ahmer BMM, Wrighton KC. Chemical and pathogen-induced inflammation disrupt the murine intestinal microbiome. MICROBIOME 2017; 5:47. [PMID: 28449706 PMCID: PMC5408407 DOI: 10.1186/s40168-017-0264-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/11/2017] [Indexed: 05/06/2023]
Abstract
BACKGROUND Salmonella is one of the most significant food-borne pathogens to affect humans and agriculture. While it is well documented that Salmonella infection triggers host inflammation, the impacts on the gut environment are largely unknown. A CBA/J mouse model was used to evaluate intestinal responses to Salmonella-induced inflammation. In parallel, we evaluated chemically induced inflammation by dextran sodium sulfate (DSS) and a non-inflammation control. We profiled gut microbial diversity by sequencing 16S ribosomal ribonucleic acid (rRNA) genes from fecal and cecal samples. These data were correlated to the inflammation marker lipocalin-2 and short-chain fatty acid concentrations. RESULTS We demonstrated that inflammation, chemically or biologically induced, restructures the chemical and microbial environment of the gut over a 16-day period. We observed that the ten mice within the Salmonella treatment group had a variable Salmonella relative abundance, with three high responding mice dominated by >46% Salmonella at later time points and the remaining seven mice denoted as low responders. These low- and high-responding Salmonella groups, along with the chemical DSS treatment, established an inflammation gradient with chemical and low levels of Salmonella having at least 3 log-fold lower lipocalin-2 concentration than the high-responding Salmonella mice. Total short-chain fatty acid and individual butyrate concentrations each negatively correlated with inflammation levels. Microbial communities were also structured along this inflammation gradient. Low levels of inflammation, regardless of chemical or biological induction, enriched for Akkermansia spp. in the Verrucomicrobiaceae and members of the Bacteroidetes family S24-7. Relative to the control or low inflammation groups, high levels of Salmonella drastically decreased the overall microbial diversity, specifically driven by the reduction of Alistipes and Lachnospiraceae in the Bacteroidetes and Firmicutes phyla, respectively. Conversely, members of the Enterobacteriaceae and Lactobacillus were positively correlated to high levels of Salmonella-induced inflammation. CONCLUSIONS Our results show that enteropathogenic infection and intestinal inflammation are interrelated factors modulating gut homeostasis. These findings may prove informative with regard to prophylactic or therapeutic strategies to prevent disruption of microbial communities, or promote their restoration.
Collapse
Affiliation(s)
- Mikayla A. Borton
- Department of Microbiology, The Ohio State University, 484 W. 12th Avenue, 440 Biological Sciences Building, Columbus, OH 43210 USA
| | - Anice Sabag-Daigle
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210 USA
- Center for Microbial Interface Biology, The Ohio State University, Columbus, OH 43210 USA
| | - Jikang Wu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210 USA
| | - Lindsey M. Solden
- Department of Microbiology, The Ohio State University, 484 W. 12th Avenue, 440 Biological Sciences Building, Columbus, OH 43210 USA
| | - Bridget S. O’Banion
- Department of Microbiology, The Ohio State University, 484 W. 12th Avenue, 440 Biological Sciences Building, Columbus, OH 43210 USA
| | - Rebecca A. Daly
- Department of Microbiology, The Ohio State University, 484 W. 12th Avenue, 440 Biological Sciences Building, Columbus, OH 43210 USA
| | - Richard A. Wolfe
- Department of Microbiology, The Ohio State University, 484 W. 12th Avenue, 440 Biological Sciences Building, Columbus, OH 43210 USA
| | - Juan F. Gonzalez
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210 USA
- Center for Microbial Interface Biology, The Ohio State University, Columbus, OH 43210 USA
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210 USA
| | - Brian M. M. Ahmer
- Department of Microbiology, The Ohio State University, 484 W. 12th Avenue, 440 Biological Sciences Building, Columbus, OH 43210 USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210 USA
- Center for Microbial Interface Biology, The Ohio State University, Columbus, OH 43210 USA
| | - Kelly C. Wrighton
- Department of Microbiology, The Ohio State University, 484 W. 12th Avenue, 440 Biological Sciences Building, Columbus, OH 43210 USA
| |
Collapse
|
54
|
Tanner AW, Carabetta VJ, Martinie RJ, Mashruwala AA, Boyd JM, Krebs C, Dubnau D. The RicAFT (YmcA-YlbF-YaaT) complex carries two [4Fe-4S] 2+ clusters and may respond to redox changes. Mol Microbiol 2017; 104:837-850. [PMID: 28295778 DOI: 10.1111/mmi.13667] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2017] [Indexed: 01/10/2023]
Abstract
During times of environmental insult, Bacillus subtilis undergoes developmental changes leading to biofilm formation, sporulation and competence. Each of these states is regulated in part by the phosphorylated form of the master response regulator Spo0A (Spo0A∼P). The phosphorylation state of Spo0A is controlled by a multi-component phosphorelay. RicA, RicF and RicT (previously YmcA, YlbF and YaaT) have been shown to be important regulatory proteins for multiple developmental fates. These proteins directly interact and form a stable complex, which has been proposed to accelerate the phosphorelay. Indeed, this complex is sufficient to stimulate the rate of phosphotransfer amongst the phosphorelay proteins in vitro. In this study, we demonstrate that two [4Fe-4S]2+ clusters can be assembled on the complex. As with other iron-sulfur cluster-binding proteins, the complex was also found to bind FAD, hinting that these cofactors may be involved in sensing the cellular redox state. This work provides the first comprehensive characterization of an iron-sulfur protein complex that regulates Spo0A∼P levels. Phylogenetic and genetic evidence suggests that the complex plays a broader role beyond stimulation of the phosphorelay.
Collapse
Affiliation(s)
- Andrew W Tanner
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Valerie J Carabetta
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA.,Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Ryan J Martinie
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Ameya A Mashruwala
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Jeffrey M Boyd
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - David Dubnau
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA.,Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| |
Collapse
|
55
|
Poehlein A, Solano JDM, Flitsch SK, Krabben P, Winzer K, Reid SJ, Jones DT, Green E, Minton NP, Daniel R, Dürre P. Microbial solvent formation revisited by comparative genome analysis. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:58. [PMID: 28286553 PMCID: PMC5343299 DOI: 10.1186/s13068-017-0742-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 02/28/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND Microbial formation of acetone, isopropanol, and butanol is largely restricted to bacteria belonging to the genus Clostridium. This ability has been industrially exploited over the last 100 years. The solvents are important feedstocks for the chemical and biofuel industry. However, biological synthesis suffers from high substrate costs and competition from chemical synthesis supported by the low price of crude oil. To render the biotechnological production economically viable again, improvements in microbial and fermentation performance are necessary. However, no comprehensive comparisons of respective species and strains used and their specific abilities exist today. RESULTS The genomes of a total 30 saccharolytic Clostridium strains, representative of the species Clostridium acetobutylicum, C. aurantibutyricum, C. beijerinckii, C. diolis, C. felsineum, C. pasteurianum, C. puniceum, C. roseum, C. saccharobutylicum, and C. saccharoperbutylacetonicum, have been determined; 10 of them completely, and compared to 14 published genomes of other solvent-forming clostridia. Two major groups could be differentiated and several misclassified species were detected. CONCLUSIONS Our findings represent a comprehensive study of phylogeny and taxonomy of clostridial solvent producers that highlights differences in energy conservation mechanisms and substrate utilization between strains, and allow for the first time a direct comparison of sequentially selected industrial strains at the genetic level. Detailed data mining is now possible, supporting the identification of new engineering targets for improved solvent production.
Collapse
Affiliation(s)
- Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - José David Montoya Solano
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Stefanie K. Flitsch
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Preben Krabben
- Green Biologics Ltd., 45A Western Avenue, Milton Park, Abingdon, Oxfordshire OX14 4RU UK
| | - Klaus Winzer
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Sharon J. Reid
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town, 7701 South Africa
| | - David T. Jones
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9010 New Zealand
| | - Edward Green
- CHAIN Biotechnology Ltd., Imperial College Incubator, Level 1 Bessemer Building, Imperial College London, London, SW7 2AZ UK
| | - Nigel P. Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Peter Dürre
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| |
Collapse
|
56
|
Xue C, Zhao J, Chen L, Yang ST, Bai F. Recent advances and state-of-the-art strategies in strain and process engineering for biobutanol production by Clostridium acetobutylicum. Biotechnol Adv 2017; 35:310-322. [DOI: 10.1016/j.biotechadv.2017.01.007] [Citation(s) in RCA: 177] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 01/06/2017] [Accepted: 01/25/2017] [Indexed: 12/20/2022]
|
57
|
Boutard M, Ettwiller L, Cerisy T, Alberti A, Labadie K, Salanoubat M, Schildkraut I, Tolonen AC. Global repositioning of transcription start sites in a plant-fermenting bacterium. Nat Commun 2016; 7:13783. [PMID: 27982035 PMCID: PMC5171806 DOI: 10.1038/ncomms13783] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/01/2016] [Indexed: 01/03/2023] Open
Abstract
Bacteria respond to their environment by regulating mRNA synthesis, often by altering the genomic sites at which RNA polymerase initiates transcription. Here, we investigate genome-wide changes in transcription start site (TSS) usage by Clostridium phytofermentans, a model bacterium for fermentation of lignocellulosic biomass. We quantify expression of nearly 10,000 TSS at single base resolution by Capp-Switch sequencing, which combines capture of synthetically capped 5' mRNA fragments with template-switching reverse transcription. We find the locations and expression levels of TSS for hundreds of genes change during metabolism of different plant substrates. We show that TSS reveals riboswitches, non-coding RNA and novel transcription units. We identify sequence motifs associated with carbon source-specific TSS and use them for regulon discovery, implicating a LacI/GalR protein in control of pectin metabolism. We discuss how the high resolution and specificity of Capp-Switch enables study of condition-specific changes in transcription initiation in bacteria.
Collapse
Affiliation(s)
- Magali Boutard
- 1CEA, DRF, IG, Genoscope, Évry 91000, France.,CNRS-UMR8030, Évry 91000, France
| | | | - Tristan Cerisy
- 1CEA, DRF, IG, Genoscope, Évry 91000, France.,CNRS-UMR8030, Évry 91000, France.,Université Paris-Saclay, Évry 91000, France.,Université d'Évry, Évry 91000, France
| | | | | | - Marcel Salanoubat
- 1CEA, DRF, IG, Genoscope, Évry 91000, France.,CNRS-UMR8030, Évry 91000, France.,Université Paris-Saclay, Évry 91000, France.,Université d'Évry, Évry 91000, France
| | - Ira Schildkraut
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Andrew C Tolonen
- 1CEA, DRF, IG, Genoscope, Évry 91000, France.,CNRS-UMR8030, Évry 91000, France.,Université Paris-Saclay, Évry 91000, France.,Université d'Évry, Évry 91000, France
| |
Collapse
|
58
|
Transcriptional analysis of degenerate strain Clostridium beijerinckii DG-8052 reveals a pleiotropic response to CaCO 3-associated recovery of solvent production. Sci Rep 2016; 6:38818. [PMID: 27966599 PMCID: PMC5155275 DOI: 10.1038/srep38818] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/14/2016] [Indexed: 12/22/2022] Open
Abstract
Degenerate Clostridium beijerinckii strain (DG-8052) can be partially recovered by supplementing CaCO3 to fermentation media. Genome resequencing of DG-8052 showed no general regulator mutated. This study focused on transcriptional analysis of DG-8052 and its response to CaCO3 treatment via microarray. The expressions of 5168 genes capturing 98.6% of C. beijerinckii NCIMB 8052 genome were examed. The results revealed that with addition of CaCO3 565 and 916 genes were significantly up-regulated, and 704 and 1044 genes significantly down-regulated at acidogenic and solventogenic phase of DG-8052, respectively. These genes are primarily responsible for glycolysis to solvent/acid production (poR, pfo), solventogensis (buk, ctf, aldh, adh, bcd) and sporulation (spo0A, sigE, sigma-70, bofA), cell motility and division (ftsA, ftsK, ftsY, ftsH, ftsE, mreB, mreC, mreD, rodA), and molecular chaperones (grpE, dnaK, dnaJ, hsp20, hsp90), etc. The functions of some altered genes in DG-8052, totalling 5.7% at acidogenisis and 8.0% at sovlentogenisis, remain unknown. The response of the degenerate strain to CaCO3 was suggested significantly pleiotropic. This study reveals the multitude of regulatory function that CaCO3 has in clostridia and provides detailed insights into degeneration mechanisms at gene regulation level. It also enables us to develop effective strategies to prevent strain degeneration in future.
Collapse
|
59
|
Bengelsdorf FR, Poehlein A, Flitsch SK, Linder S, Schiel-Bengelsdorf B, Stegmann BA, Krabben P, Green E, Zhang Y, Minton N, Dürre P. Host Organisms: Clostridium acetobutylicum/ Clostridium beijerinckiiand Related Organisms. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Frank R. Bengelsdorf
- Universität Ulm; Institut für Mikrobiologie und Biotechnologie; Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Anja Poehlein
- Georg-August University; Genomic and Applied Microbiology and Göttingen Genomics Laboratory; Göttingen, Grisebachstr. 8 37077 Göttingen Germany
| | - Stefanie K. Flitsch
- Universität Ulm; Institut für Mikrobiologie und Biotechnologie; Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Sonja Linder
- Universität Ulm; Institut für Mikrobiologie und Biotechnologie; Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Bettina Schiel-Bengelsdorf
- Universität Ulm; Institut für Mikrobiologie und Biotechnologie; Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Benjamin A. Stegmann
- Universität Ulm; Institut für Mikrobiologie und Biotechnologie; Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Preben Krabben
- Green Biologics Limited; 45A Western Avenue, Milton Park Abingdon Oxfordshire OX14 4RU UK
| | - Edward Green
- CHAIN Biotechnology Limited; Imperial College Incubator, Imperial College London; Level 1 Bessemer Building London SW7 2AZ UK
| | - Ying Zhang
- University of Nottingham; BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences; University Park Nottingham NG7 2RD UK
| | - Nigel Minton
- University of Nottingham; BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences; University Park Nottingham NG7 2RD UK
| | - Peter Dürre
- Universität Ulm; Institut für Mikrobiologie und Biotechnologie; Albert-Einstein-Allee 11 89081 Ulm Germany
| |
Collapse
|
60
|
The Phosphotransfer Protein CD1492 Represses Sporulation Initiation in Clostridium difficile. Infect Immun 2016; 84:3434-3444. [PMID: 27647869 DOI: 10.1128/iai.00735-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 09/12/2016] [Indexed: 12/18/2022] Open
Abstract
The formation of spores is critical for the survival of Clostridium difficile outside the host gastrointestinal tract. Persistence of C. difficile spores greatly contributes to the spread of C. difficile infection (CDI), and the resistance of spores to antimicrobials facilitates the relapse of infection. Despite the importance of sporulation to C. difficile pathogenesis, the molecular mechanisms controlling spore formation are not well understood. The initiation of sporulation is known to be regulated through activation of the conserved transcription factor Spo0A. Multiple regulators influence Spo0A activation in other species; however, many of these factors are not conserved in C. difficile and few novel factors have been identified. Here, we investigated the function of a protein, CD1492, that is annotated as a kinase and was originally proposed to promote sporulation by directly phosphorylating Spo0A. We found that deletion of CD1492 resulted in increased sporulation, indicating that CD1492 is a negative regulator of sporulation. Accordingly, we observed increased transcription of Spo0A-dependent genes in the CD1492 mutant. Deletion of CD1492 also resulted in decreased toxin production in vitro and in decreased virulence in the hamster model of CDI. Further, the CD1492 mutant demonstrated effects on gene expression that are not associated with Spo0A activation, including lower sigD and rstA transcription, suggesting that this protein interacts with factors other than Spo0A. Altogether, the data indicate that CD1492 negatively affects sporulation and positively influences motility and virulence. These results provide further evidence that C. difficile sporulation is regulated differently from that of other endospore-forming species.
Collapse
|
61
|
Edwards AN, Karim ST, Pascual RA, Jowhar LM, Anderson SE, McBride SM. Chemical and Stress Resistances of Clostridium difficile Spores and Vegetative Cells. Front Microbiol 2016; 7:1698. [PMID: 27833595 PMCID: PMC5080291 DOI: 10.3389/fmicb.2016.01698] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/12/2016] [Indexed: 12/11/2022] Open
Abstract
Clostridium difficile is a Gram-positive, sporogenic and anaerobic bacterium that causes a potentially fatal colitis. C. difficile enters the body as dormant spores that germinate in the colon to form vegetative cells that secrete toxins and cause the symptoms of infection. During transit through the intestine, some vegetative cells transform into spores, which are more resistant to killing by environmental insults than the vegetative cells. Understanding the inherent resistance properties of the vegetative and spore forms of C. difficile is imperative for the development of methods to target and destroy the bacterium. The objective of this study was to define the chemical and environmental resistance properties of C. difficile vegetative cells and spores. We examined vegetative cell and spore tolerances of three C. difficile strains, including 630Δerm, a 012 ribotype and a derivative of a past epidemic strain; R20291, a 027 ribotype and current epidemic strain; and 5325, a clinical isolate that is a 078 ribotype. All isolates were tested for tolerance to ethanol, oxygen, hydrogen peroxide, butanol, chloroform, heat and sodium hypochlorite (household bleach). Our results indicate that 630Δerm vegetative cells (630 spo0A) are more resistant to oxidative stress than those of R20291 (R20291 spo0A) and 5325 (5325 spo0A). In addition, 5325 spo0A vegetative cells exhibited greater resistance to organic solvents. In contrast, 630Δerm spores were more sensitive than R20291 or 5325 spores to butanol. Spores from all three strains exhibited high levels of resistance to ethanol, hydrogen peroxide, chloroform and heat, although R20291 spores were more resistant to temperatures in the range of 60-75°C. Finally, household bleach served as the only chemical reagent tested that consistently reduced C. difficile vegetative cells and spores of all tested strains. These findings establish conditions that result in vegetative cell and spore elimination and illustrate the resistance of C. difficile to common decontamination methods. These results further demonstrate that the vegetative cells and spores of various C. difficile strains have different resistance properties that may impact decontamination of surfaces and hands.
Collapse
Affiliation(s)
- Adrianne N Edwards
- Emory Antibiotic Resistance Center, Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta GA, USA
| | - Samiha T Karim
- Emory Antibiotic Resistance Center, Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta GA, USA
| | - Ricardo A Pascual
- Emory Antibiotic Resistance Center, Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta GA, USA
| | - Lina M Jowhar
- Emory Antibiotic Resistance Center, Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta GA, USA
| | - Sarah E Anderson
- Emory Antibiotic Resistance Center, Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta GA, USA
| | - Shonna M McBride
- Emory Antibiotic Resistance Center, Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta GA, USA
| |
Collapse
|
62
|
Koonin EV, Starokadomskyy P. Are viruses alive? The replicator paradigm sheds decisive light on an old but misguided question. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2016; 59:125-34. [PMID: 26965225 PMCID: PMC5406846 DOI: 10.1016/j.shpsc.2016.02.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 02/27/2016] [Indexed: 05/18/2023]
Abstract
The question whether or not "viruses are alive" has caused considerable debate over many years. Yet, the question is effectively without substance because the answer depends entirely on the definition of life or the state of "being alive" that is bound to be arbitrary. In contrast, the status of viruses among biological entities is readily defined within the replicator paradigm. All biological replicators form a continuum along the selfishness-cooperativity axis, from the completely selfish to fully cooperative forms. Within this range, typical, lytic viruses represent the selfish extreme whereas temperate viruses and various mobile elements occupy positions closer to the middle of the range. Selfish replicators not only belong to the biological realm but are intrinsic to any evolving system of replicators. No such system can evolve without the emergence of parasites, and moreover, parasites drive the evolution of biological complexity at multiple levels. The history of life is a story of parasite-host coevolution that includes both the incessant arms race and various forms of cooperation. All organisms are communities of interacting, coevolving replicators of different classes. A complete theory of replicator coevolution remains to be developed, but it appears likely that not only the differentiation between selfish and cooperative replicators but the emergence of the entire range of replication strategies, from selfish to cooperative, is intrinsic to biological evolution.
Collapse
Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Petro Starokadomskyy
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, 75235, USA
| |
Collapse
|
63
|
CodY-Dependent Regulation of Sporulation in Clostridium difficile. J Bacteriol 2016; 198:2113-30. [PMID: 27246573 DOI: 10.1128/jb.00220-16] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/22/2016] [Indexed: 01/05/2023] Open
Abstract
UNLABELLED Clostridium difficile must form a spore to survive outside the gastrointestinal tract. The factors that trigger sporulation in C. difficile remain poorly understood. Previous studies have suggested that a link exists between nutritional status and sporulation initiation in C. difficile In this study, we investigated the impact of the global nutritional regulator CodY on sporulation in C. difficile strains from the historical 012 ribotype and the current epidemic 027 ribotype. Sporulation frequencies were increased in both backgrounds, demonstrating that CodY represses sporulation in C. difficile The 027 codY mutant exhibited a greater increase in spore formation than the 012 codY mutant. To determine the role of CodY in the observed sporulation phenotypes, we examined several factors that are known to influence sporulation in C. difficile Using transcriptional reporter fusions and quantitative reverse transcription-PCR (qRT-PCR) analysis, we found that two loci associated with the initiation of sporulation, opp and sinR, are regulated by CodY. The data demonstrate that CodY is a repressor of sporulation in C. difficile and that the impact of CodY on sporulation and expression of specific genes is significantly influenced by the strain background. These results suggest that the variability of CodY-dependent regulation is an important contributor to virulence and sporulation in current epidemic isolates. This report provides further evidence that nutritional state, virulence, and sporulation are linked in C. difficile IMPORTANCE This study sought to examine the relationship between nutrition and sporulation in C. difficile by examining the global nutritional regulator CodY. CodY is a known virulence and nutritional regulator of C. difficile, but its role in sporulation was unknown. Here, we demonstrate that CodY is a negative regulator of sporulation in two different ribotypes of C. difficile We also demonstrate that CodY regulates known effectors of sporulation, Opp and SinR. These results support the idea that nutrient limitation is a trigger for sporulation in C. difficile and that the response to nutrient limitation is coordinated by CodY. Additionally, we demonstrate that CodY has an altered role in sporulation regulation for some strains.
Collapse
|
64
|
Kröber M, Verwaaijen B, Wibberg D, Winkler A, Pühler A, Schlüter A. Comparative transcriptome analysis of the biocontrol strain Bacillus amyloliquefaciens FZB42 as response to biofilm formation analyzed by RNA sequencing. J Biotechnol 2016; 231:212-223. [PMID: 27312701 DOI: 10.1016/j.jbiotec.2016.06.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 05/23/2016] [Accepted: 06/12/2016] [Indexed: 10/21/2022]
Abstract
The strain Bacillus amyloliquefaciens FZB42 is a plant growth promoting rhizobacterium (PGPR) and biocontrol agent known to keep infections of lettuce (Lactuca sativa) by the phytopathogen Rhizoctonia solani down. Several mechanisms, including the production of secondary metabolites possessing antimicrobial properties and induction of the host plant's systemic resistance (ISR), were proposed to explain the biocontrol effect of the strain. B. amyloliquefaciens FZB42 is able to form plaques (biofilm-like structures) on plant roots and this feature was discussed to be associated with its biocontrol properties. For this reason, formation of B. amyloliquefaciens biofilms was studied at the transcriptional level using high-throughput sequencing of whole transcriptome cDNA libraries from cells grown under biofilm-forming conditions vs. planktonic growth. Comparison of the transcriptional profiles of B. amyloliquefaciens FZB42 under these growth conditions revealed a common set of highly transcribed genes mostly associated with basic cellular functions. The lci gene, encoding an antimicrobial peptide (AMP), was among the most highly transcribed genes of cells under both growth conditions suggesting that AMP production may contribute to biocontrol. In contrast, gene clusters coding for synthesis of secondary metabolites with antimicrobial properties were only moderately transcribed and not induced in biofilm-forming cells. Differential gene expression revealed that 331 genes were significantly up-regulated and 230 genes were down-regulated in the transcriptome of B. amyloliquefaciens FZB42 under biofilm-forming conditions in comparison to planktonic cells. Among the most highly up-regulated genes, the yvqHI operon, coding for products involved in nisin (class I bacteriocin) resistance, was identified. In addition, an operon whose products play a role in fructosamine metabolism was enhanced in its transcription. Moreover, genes involved in the production of the extracellular biofilm matrix including exopolysaccharide genes (eps) and the yqxM-tasA-sipW operon encoding amyloid fiber synthesis were up-regulated in the B. amyloliquefaciens FZB42 biofilm. On the other hand, highly down-regulated genes in biofilms are associated with synthesis, assembly and regulation of the flagellar apparatus, the degradation of aromatic compounds and the export of copper. The obtained transcriptional profile for B. amyloliquefaciens biofilm cells uncovered genes involved in its development and enabled the assessment that synthesis of secondary metabolites among other factors may contribute to the biocontrol properties of the strain.
Collapse
Affiliation(s)
- Magdalena Kröber
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Bart Verwaaijen
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Daniel Wibberg
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Anika Winkler
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Alfred Pühler
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andreas Schlüter
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
| |
Collapse
|
65
|
Deciphering Clostridium tyrobutyricum Metabolism Based on the Whole-Genome Sequence and Proteome Analyses. mBio 2016; 7:mBio.00743-16. [PMID: 27302759 PMCID: PMC4916380 DOI: 10.1128/mbio.00743-16] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Clostridium tyrobutyricum is a Gram-positive anaerobic bacterium that efficiently produces butyric acid and is considered a promising host for anaerobic production of bulk chemicals. Due to limited knowledge on the genetic and metabolic characteristics of this strain, however, little progress has been made in metabolic engineering of this strain. Here we report the complete genome sequence of C. tyrobutyricum KCTC 5387 (ATCC 25755), which consists of a 3.07-Mbp chromosome and a 63-kbp plasmid. The results of genomic analyses suggested that C. tyrobutyricum produces butyrate from butyryl-coenzyme A (butyryl-CoA) through acetate reassimilation by CoA transferase, differently from Clostridium acetobutylicum, which uses the phosphotransbutyrylase-butyrate kinase pathway; this was validated by reverse transcription-PCR (RT-PCR) of related genes, protein expression levels, in vitro CoA transferase assay, and fed-batch fermentation. In addition, the changes in protein expression levels during the course of batch fermentations on glucose were examined by shotgun proteomics. Unlike C. acetobutylicum, the expression levels of proteins involved in glycolytic and fermentative pathways in C. tyrobutyricum did not decrease even at the stationary phase. Proteins related to energy conservation mechanisms, including Rnf complex, NfnAB, and pyruvate-phosphate dikinase that are absent in C. acetobutylicum, were identified. Such features explain why this organism can produce butyric acid to a much higher titer and better tolerate toxic metabolites. This study presenting the complete genome sequence, global protein expression profiles, and genome-based metabolic characteristics during the batch fermentation of C. tyrobutyricum will be valuable in designing strategies for metabolic engineering of this strain. IMPORTANCE Bio-based production of chemicals from renewable biomass has become increasingly important due to our concerns on climate change and other environmental problems. C. tyrobutyricum has been used for efficient butyric acid production. In order to further increase the performance and expand the capabilities of this strain toward production of other chemicals, metabolic engineering needs to be performed. For this, better understanding on the metabolic and physiological characteristics of this bacterium at the genome level is needed. This work reporting the results of complete genomic and proteomic analyses together with new insights on butyric acid biosynthetic pathway and energy conservation will allow development of strategies for metabolic engineering of C. tyrobutyricum for the bio-based production of various chemicals in addition to butyric acid.
Collapse
|
66
|
Martin-Verstraete I, Peltier J, Dupuy B. The Regulatory Networks That Control Clostridium difficile Toxin Synthesis. Toxins (Basel) 2016; 8:E153. [PMID: 27187475 PMCID: PMC4885068 DOI: 10.3390/toxins8050153] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 05/03/2016] [Accepted: 05/05/2016] [Indexed: 12/19/2022] Open
Abstract
The pathogenic clostridia cause many human and animal diseases, which typically arise as a consequence of the production of potent exotoxins. Among the enterotoxic clostridia, Clostridium difficile is the main causative agent of nosocomial intestinal infections in adults with a compromised gut microbiota caused by antibiotic treatment. The symptoms of C. difficile infection are essentially caused by the production of two exotoxins: TcdA and TcdB. Moreover, for severe forms of disease, the spectrum of diseases caused by C. difficile has also been correlated to the levels of toxins that are produced during host infection. This observation strengthened the idea that the regulation of toxin synthesis is an important part of C. difficile pathogenesis. This review summarizes our current knowledge about the regulators and sigma factors that have been reported to control toxin gene expression in response to several environmental signals and stresses, including the availability of certain carbon sources and amino acids, or to signaling molecules, such as the autoinducing peptides of quorum sensing systems. The overlapping regulation of key metabolic pathways and toxin synthesis strongly suggests that toxin production is a complex response that is triggered by bacteria in response to particular states of nutrient availability during infection.
Collapse
Affiliation(s)
- Isabelle Martin-Verstraete
- Laboratoire Pathogenèse des Bactéries Anaérobes, Department of Microbiology, Institut Pasteur, 25 rue du Dr Roux Paris, Paris 75015, France.
- UFR Sciences du vivant, University Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris 75015, France.
| | - Johann Peltier
- Laboratoire Pathogenèse des Bactéries Anaérobes, Department of Microbiology, Institut Pasteur, 25 rue du Dr Roux Paris, Paris 75015, France.
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobes, Department of Microbiology, Institut Pasteur, 25 rue du Dr Roux Paris, Paris 75015, France.
| |
Collapse
|
67
|
Transcriptional Profile during Deoxycholate-Induced Sporulation in a Clostridium perfringens Isolate Causing Foodborne Illness. Appl Environ Microbiol 2016; 82:2929-2942. [PMID: 26969700 DOI: 10.1128/aem.00252-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 03/03/2016] [Indexed: 01/05/2023] Open
Abstract
UNLABELLED Clostridium perfringens type A is a common source of foodborne illness (FBI) in humans. Vegetative cells sporulate in the small intestinal tract and produce the major pathogenic factor C. perfringens enterotoxin. Although sporulation plays a critical role in the pathogenesis of FBI, the mechanisms inducing sporulation remain unclear. Bile salts were shown previously to induce sporulation, and we confirmed deoxycholate (DCA)-induced sporulation in C. perfringens strain NCTC8239 cocultured with human intestinal epithelial Caco-2 cells. In the present study, we performed transcriptome analyses of strain NCTC8239 in order to elucidate the mechanism underlying DCA-induced sporulation. Of the 2,761 genes analyzed, 333 were up- or downregulated during DCA-induced sporulation and included genes for cell division, nutrient metabolism, signal transduction, and defense mechanisms. In contrast, the virulence-associated transcriptional regulators (the VirR/VirS system, the agr system, codY, and abrB) were not activated by DCA. DCA markedly increased the expression of signaling molecules controlled by Spo0A, the master regulator of the sporulation process, whereas the expression of spo0A itself was not altered in the presence or absence of DCA. The phosphorylation of Spo0A was enhanced in the presence of DCA. Collectively, these results demonstrated that DCA induced sporulation, at least partially, by facilitating the phosphorylation of Spo0A and activating Spo0A-regulated genes in strain NCTC8239 while altering the expression of various genes. IMPORTANCE Disease caused by Clostridium perfringens type A consistently ranks among the most common bacterial foodborne illnesses in humans in developed countries. The sporulation of C. perfringens in the small intestinal tract is a key event for its pathogenesis, but the factors and underlying mechanisms by which C. perfringens sporulates in vivo currently remain unclear. Bile salts, major components of bile, which is secreted from the liver for the emulsification of lipids, were shown to induce sporulation. However, the mechanisms underlying bile salt-induced sporulation have not yet been clarified. In the present study, we demonstrate that deoxycholate (one of the bile salts) induces sporulation by facilitating the phosphorylation of Spo0A and activating Spo0A-regulated genes using a transcriptome analysis. Thus, this study enhances our understanding of the mechanisms underlying sporulation, particularly that of bile salt-induced sporulation, in C. perfringens.
Collapse
|
68
|
Kirsebom LA, Dasgupta S, Fredrik Pettersson BM. Pleiomorphism in Mycobacterium. ADVANCES IN APPLIED MICROBIOLOGY 2016; 80:81-112. [PMID: 22794145 DOI: 10.1016/b978-0-12-394381-1.00004-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Morphological variants in mycobacterial cultures under different growth conditions, including aging of the culture, have been shown to include fibrous aggregates, biofilms, coccoids, and spores. Here we discuss the diversity in shape and size changes demonstrated by bacterial cells with special reference to pleiomorphism observed in Mycobacterium spp. in response to nutritional and other environmental stresses. Inherent asymmetry in cell division and compartmentalization of cell interior under different growth conditions might contribute toward the observed pleiomorphism in mycobacteria. The regulatory genes comprising the bacterial signaling pathway responsible for initiating morphogenesis are speculated upon from bioinformatic identifications of genes for known sensors, kinases, and phosphatases existing in mycobacterial genomes as well as on the basis of what is known in other bacteria.
Collapse
|
69
|
Liao C, Seo SO, Lu T. System-level modeling of acetone-butanol-ethanol fermentation. FEMS Microbiol Lett 2016; 363:fnw074. [PMID: 27020410 DOI: 10.1093/femsle/fnw074] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2016] [Indexed: 11/12/2022] Open
Abstract
Acetone-butanol-ethanol (ABE) fermentation is a metabolic process of clostridia that produces bio-based solvents including butanol. It is enabled by an underlying metabolic reaction network and modulated by cellular gene regulation and environmental cues. Mathematical modeling has served as a valuable strategy to facilitate the understanding, characterization and optimization of this process. In this review, we highlight recent advances in system-level, quantitative modeling of ABE fermentation. We begin with an overview of integrative processes underlying the fermentation. Next we survey modeling efforts including early simple models, models with a systematic metabolic description, and those incorporating metabolism through simple gene regulation. Particular focus is given to a recent system-level model that integrates the metabolic reactions, gene regulation and environmental cues. We conclude by discussing the remaining challenges and future directions towards predictive understanding of ABE fermentation.
Collapse
Affiliation(s)
- Chen Liao
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Seung-Oh Seo
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - Ting Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
70
|
The Role of Bacterial Spores in Metal Cycling and Their Potential Application in Metal Contaminant Bioremediation. Microbiol Spectr 2016; 4. [DOI: 10.1128/microbiolspec.tbs-0018-2013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
ABSTRACT
Bacteria are one of the premier biological forces that, in combination with chemical and physical forces, drive metal availability in the environment. Bacterial spores, when found in the environment, are often considered to be dormant and metabolically inactive, in a resting state waiting for favorable conditions for them to germinate. However, this is a highly oversimplified view of spores in the environment. The surface of bacterial spores represents a potential site for chemical reactions to occur. Additionally, proteins in the outer layers (spore coats or exosporium) may also have more specific catalytic activity. As a consequence, bacterial spores can play a role in geochemical processes and may indeed find uses in various biotechnological applications. The aim of this review is to introduce the role of bacteria and bacterial spores in biogeochemical cycles and their potential use as toxic metal bioremediation agents.
Collapse
|
71
|
Edwards AN, Tamayo R, McBride SM. A novel regulator controls Clostridium difficile sporulation, motility and toxin production. Mol Microbiol 2016; 100:954-71. [PMID: 26915493 DOI: 10.1111/mmi.13361] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2016] [Indexed: 01/09/2023]
Abstract
Clostridium difficile is an anaerobic pathogen that forms spores which promote survival in the environment and transmission to new hosts. The regulatory pathways by which C. difficile initiates spore formation are poorly understood. We identified two factors with limited similarity to the Rap sporulation proteins of other spore-forming bacteria. In this study, we show that disruption of the gene CD3668 reduces sporulation and increases toxin production and motility. This mutant was more virulent and exhibited increased toxin gene expression in the hamster model of infection. Based on these phenotypes, we have renamed this locus rstA, for regulator of sporulation and toxins. Our data demonstrate that RstA is a bifunctional protein that upregulates sporulation through an unidentified pathway and represses motility and toxin production by influencing sigD transcription. Conserved RstA orthologs are present in other pathogenic and industrial Clostridium species and may represent a key regulatory protein controlling clostridial sporulation.
Collapse
Affiliation(s)
- Adrianne N Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shonna M McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| |
Collapse
|
72
|
Wells-Bennik MH, Eijlander RT, den Besten HM, Berendsen EM, Warda AK, Krawczyk AO, Nierop Groot MN, Xiao Y, Zwietering MH, Kuipers OP, Abee T. Bacterial Spores in Food: Survival, Emergence, and Outgrowth. Annu Rev Food Sci Technol 2016; 7:457-82. [DOI: 10.1146/annurev-food-041715-033144] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Marjon H.J. Wells-Bennik
- TI Food and Nutrition, 6700 AN Wageningen, The Netherlands
- NIZO Food Research, 6718 ZB Ede, The Netherlands;
| | - Robyn T. Eijlander
- TI Food and Nutrition, 6700 AN Wageningen, The Netherlands
- NIZO Food Research, 6718 ZB Ede, The Netherlands;
| | - Heidy M.W. den Besten
- TI Food and Nutrition, 6700 AN Wageningen, The Netherlands
- Laboratory of Food Microbiology, Wageningen University, 6700 AA Wageningen, The Netherlands
| | - Erwin M. Berendsen
- TI Food and Nutrition, 6700 AN Wageningen, The Netherlands
- NIZO Food Research, 6718 ZB Ede, The Netherlands;
- Molecular Genetics Department, University of Groningen, 9700 AB Groningen, The Netherlands
| | - Alicja K. Warda
- TI Food and Nutrition, 6700 AN Wageningen, The Netherlands
- Laboratory of Food Microbiology, Wageningen University, 6700 AA Wageningen, The Netherlands
- Wageningen UR Food & Biobased Research, 6700 AA Wageningen, The Netherlands
| | - Antonina O. Krawczyk
- TI Food and Nutrition, 6700 AN Wageningen, The Netherlands
- Molecular Genetics Department, University of Groningen, 9700 AB Groningen, The Netherlands
| | - Masja N. Nierop Groot
- TI Food and Nutrition, 6700 AN Wageningen, The Netherlands
- Wageningen UR Food & Biobased Research, 6700 AA Wageningen, The Netherlands
| | - Yinghua Xiao
- TI Food and Nutrition, 6700 AN Wageningen, The Netherlands
- Laboratory of Food Microbiology, Wageningen University, 6700 AA Wageningen, The Netherlands
| | - Marcel H. Zwietering
- TI Food and Nutrition, 6700 AN Wageningen, The Netherlands
- Laboratory of Food Microbiology, Wageningen University, 6700 AA Wageningen, The Netherlands
| | - Oscar P. Kuipers
- TI Food and Nutrition, 6700 AN Wageningen, The Netherlands
- Molecular Genetics Department, University of Groningen, 9700 AB Groningen, The Netherlands
| | - Tjakko Abee
- TI Food and Nutrition, 6700 AN Wageningen, The Netherlands
- Laboratory of Food Microbiology, Wageningen University, 6700 AA Wageningen, The Netherlands
| |
Collapse
|
73
|
Abstract
Endospore formation follows a complex, highly regulated developmental pathway that occurs in a broad range of Firmicutes. Although Bacillus subtilis has served as a powerful model system to study the morphological, biochemical, and genetic determinants of sporulation, fundamental aspects of the program remain mysterious for other genera. For example, it is entirely unknown how most lineages within the Firmicutes regulate entry into sporulation. Additionally, little is known about how the sporulation pathway has evolved novel spore forms and reproductive schemes. Here, we describe endospore and internal offspring development in diverse Firmicutes and outline progress in characterizing these programs. Moreover, comparative genomics studies are identifying highly conserved sporulation genes, and predictions of sporulation potential in new isolates and uncultured bacteria can be made from these data. One surprising outcome of these comparative studies is that core regulatory and some structural aspects of the program appear to be universally conserved. This suggests that a robust and sophisticated developmental framework was already in place in the last common ancestor of all extant Firmicutes that produce internal offspring or endospores. The study of sporulation in model systems beyond B. subtilis will continue to provide key information on the flexibility of the program and provide insights into how changes in this developmental course may confer advantages to cells in diverse environments.
Collapse
|
74
|
Willing SE, Richards EJ, Sempere L, Dale AG, Cutting SM, Fairweather NF. Increased toxin expression in a Clostridium difficile mfd mutant. BMC Microbiol 2015; 15:280. [PMID: 26679502 PMCID: PMC4683965 DOI: 10.1186/s12866-015-0611-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 12/03/2015] [Indexed: 12/18/2022] Open
Abstract
Background The symptoms of Clostridium difficile infection are mediated primarily by two toxins, TcdA and TcdB, the expression of which is governed by a multitude of factors including nutrient availability, growth phase and cell stress. Several global regulators have been implicated in the regulation of toxin expression, such as CcpA and CodY. Results During attempts to insertionally inactivate a putative secondary cell wall polysaccharide synthesis gene, we obtained several mutants containing off-target insertions. One mutant displayed an unusual branched colony morphology and was investigated further. Marker recovery revealed an insertion in mfd, a gene encoding a transcription-coupled repair factor. The mfd mutant exhibited pleiotropic effects, in particular increased expression of both toxin A and B (TcdA and TcdB) compared to the parental strain. Western blotting and cellular cytotoxicity assays revealed increased expression across all time points over a 24 h period, with inactivation of mfd resulting in at least a 10 fold increase in cell cytotoxicity. qRT-PCR demonstrated the upregulation of both toxins occurred on a transcriptional level. All effects of the mfd mutation were complemented by a plasmid-encoded copy of mfd, showing the effects are not due to polar effects of the intron insertion or to second site mutations. Conclusions This study adds Mfd to the repertoire of factors involved in regulation of toxin expression in Clostridium difficile. Mfd is known to remove RNA polymerase molecules from transcriptional sites where it has stalled due to repressor action, preventing transcriptional read through. The consistently high levels of toxin in the C. difficile mfd mutant indicate this process is inefficient leading to transcriptional de-repression.
Collapse
Affiliation(s)
- Stephanie E Willing
- Department of Life Sciences, Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK. .,School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK.
| | - Emma J Richards
- Department of Life Sciences, Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK.
| | - Lluis Sempere
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK.
| | - Aaron G Dale
- Department of Life Sciences, Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK.
| | - Simon M Cutting
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK.
| | - Neil F Fairweather
- Department of Life Sciences, Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK.
| |
Collapse
|
75
|
Wynendaele E, Verbeke F, Stalmans S, Gevaert B, Janssens Y, Van De Wiele C, Peremans K, Burvenich C, De Spiegeleer B. Quorum Sensing Peptides Selectively Penetrate the Blood-Brain Barrier. PLoS One 2015; 10:e0142071. [PMID: 26536593 PMCID: PMC4633044 DOI: 10.1371/journal.pone.0142071] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/17/2015] [Indexed: 12/30/2022] Open
Abstract
Bacteria communicate with each other by the use of signaling molecules, a process called 'quorum sensing'. One group of quorum sensing molecules includes the oligopeptides, which are mainly produced by Gram-positive bacteria. Recently, these quorum sensing peptides were found to biologically influence mammalian cells, promoting i.a. metastasis of cancer cells. Moreover, it was found that bacteria can influence different central nervous system related disorders as well, e.g. anxiety, depression and autism. Research currently focuses on the role of bacterial metabolites in this bacteria-brain interaction, with the role of the quorum sensing peptides not yet known. Here, three chemically diverse quorum sensing peptides were investigated for their brain influx (multiple time regression technique) and efflux properties in an in vivo mouse model (ICR-CD-1) to determine blood-brain transfer properties: PhrCACET1 demonstrated comparatively a very high initial influx into the mouse brain (Kin = 20.87 μl/(g×min)), while brain penetrabilities of BIP-2 and PhrANTH2 were found to be low (Kin = 2.68 μl/(g×min)) and very low (Kin = 0.18 μl/(g×min)), respectively. All three quorum sensing peptides were metabolically stable in plasma (in vitro) during the experimental time frame and no significant brain efflux was observed. Initial tissue distribution data showed remarkably high liver accumulation of BIP-2 as well. Our results thus support the potential role of some quorum sensing peptides in different neurological disorders, thereby enlarging our knowledge about the microbiome-brain axis.
Collapse
Affiliation(s)
- Evelien Wynendaele
- Drug Quality and Registration (DruQuaR) group, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Frederick Verbeke
- Drug Quality and Registration (DruQuaR) group, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Sofie Stalmans
- Drug Quality and Registration (DruQuaR) group, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Bert Gevaert
- Drug Quality and Registration (DruQuaR) group, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Yorick Janssens
- Drug Quality and Registration (DruQuaR) group, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Christophe Van De Wiele
- Department of Radiology and Nuclear Medicine, Faculty of Medicine and Health Sciences, Ghent University Hospital, Ghent, Belgium
| | - Kathelijne Peremans
- Department of Medical Imaging, Medicine and Clinical Biology of Small Animals, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Christian Burvenich
- Comparative Physiology and Biometrics, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Bart De Spiegeleer
- Drug Quality and Registration (DruQuaR) group, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| |
Collapse
|
76
|
Abstract
Formation of heat-resistant endospores is a specific property of the members of the phylum Firmicutes (low-G+C Gram-positive bacteria). It is found in representatives of four different classes of Firmicutes, Bacilli, Clostridia, Erysipelotrichia, and Negativicutes, which all encode similar sets of core sporulation proteins. Each of these classes also includes non-spore-forming organisms that sometimes belong to the same genus or even species as their spore-forming relatives. This chapter reviews the diversity of the members of phylum Firmicutes, its current taxonomy, and the status of genome-sequencing projects for various subgroups within the phylum. It also discusses the evolution of the Firmicutes from their apparently spore-forming common ancestor and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, ruminococci) in the course of their adaptation to the saprophytic lifestyle in a nutrient-rich environment. It argues that the systematics of Firmicutes is a rapidly developing area of research that benefits from the evolutionary approaches to the ever-increasing amount of genomic and phenotypic data and allows arranging these data into a common framework.
Collapse
|
77
|
Abstract
Microbes transiently differentiate into distinct, specialized cell types to generate functional diversity and cope with changing environmental conditions. Though alternate programs often entail radically different physiological and morphological states, recent single-cell studies have revealed that these crucial decisions are often left to chance. In these cases, the underlying genetic circuits leverage the intrinsic stochasticity of intracellular chemistry to drive transition between states. Understanding how these circuits transform transient gene expression fluctuations into lasting phenotypic programs will require a combination of quantitative modeling and extensive, time-resolved observation of switching events in single cells. In this article, we survey microbial cell fate decisions demonstrated to involve a random element, describe theoretical frameworks for understanding stochastic switching between states, and highlight recent advances in microfluidics that will enable characterization of key dynamic features of these circuits.
Collapse
Affiliation(s)
- Thomas M Norman
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115; , ,
| | - Nathan D Lord
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115; , ,
| | - Johan Paulsson
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115; , ,
| | - Richard Losick
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138;
| |
Collapse
|
78
|
Jia N, Du J, Ding MZ, Gao F, Yuan YJ. Genome Sequence of Bacillus endophyticus and Analysis of Its Companion Mechanism in the Ketogulonigenium vulgare-Bacillus Strain Consortium. PLoS One 2015; 10:e0135104. [PMID: 26248285 PMCID: PMC4527741 DOI: 10.1371/journal.pone.0135104] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 07/16/2015] [Indexed: 11/19/2022] Open
Abstract
Bacillus strains have been widely used as the companion strain of Ketogulonigenium vulgare in the process of vitamin C fermentation. Different Bacillus strains generate different effects on the growth of K. vulgare and ultimately influence the productivity. First, we identified that Bacillus endophyticus Hbe603 was an appropriate strain to cooperate with K. vulgare and the product conversion rate exceeded 90% in industrial vitamin C fermentation. Here, we report the genome sequencing of the B. endophyticus Hbe603 industrial companion strain and speculate its possible advantage in the consortium. The circular chromosome of B. endophyticus Hbe603 has a size of 4.87 Mb with GC content of 36.64% and has the highest similarity with that of Bacillus megaterium among all the bacteria with complete genomes. By comparing the distribution of COGs with that of Bacillus thuringiensis, Bacillus cereus and B. megaterium, B. endophyticus has less genes related to cell envelope biogenesis and signal transduction mechanisms, and more genes related to carbohydrate transport and metabolism, energy production and conversion, as well as lipid transport and metabolism. Genome-based functional studies revealed the specific capability of B. endophyticus in sporulation, transcription regulation, environmental resistance, membrane transportation, extracellular proteins and nutrients synthesis, which would be beneficial for K. vulgare. In particular, B. endophyticus lacks the Rap-Phr signal cascade system and, in part, spore coat related proteins. In addition, it has specific pathways for vitamin B12 synthesis and sorbitol metabolism. The genome analysis of the industrial B. endophyticus will help us understand its cooperative mechanism in the K. vulgare-Bacillus strain consortium to improve the fermentation of vitamin C.
Collapse
Affiliation(s)
- Nan Jia
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
| | - Jin Du
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
| | - Ming-Zhu Ding
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
| | - Feng Gao
- Department of Physics, Tianjin University, Tianjin, 300072, PR China
- * E-mail: (FG); (YJY)
| | - Ying-Jin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
- * E-mail: (FG); (YJY)
| |
Collapse
|
79
|
Papoutsakis ET. Reassessing the Progress in the Production of Advanced Biofuels in the Current Competitive Environment and Beyond: What Are the Successes and Where Progress Eludes Us and Why. Ind Eng Chem Res 2015. [DOI: 10.1021/acs.iecr.5b01695] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Eleftherios T. Papoutsakis
- Molecular Biotechnology Laboratory, Department of Chemical & Biomolecular Engineering, Department of Biological Sciences & the Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, United States
| |
Collapse
|
80
|
The Clostridium sporulation programs: diversity and preservation of endospore differentiation. Microbiol Mol Biol Rev 2015; 79:19-37. [PMID: 25631287 DOI: 10.1128/mmbr.00025-14] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
SUMMARY Bacillus and Clostridium organisms initiate the sporulation process when unfavorable conditions are detected. The sporulation process is a carefully orchestrated cascade of events at both the transcriptional and posttranslational levels involving a multitude of sigma factors, transcription factors, proteases, and phosphatases. Like Bacillus genomes, sequenced Clostridium genomes contain genes for all major sporulation-specific transcription and sigma factors (spo0A, sigH, sigF, sigE, sigG, and sigK) that orchestrate the sporulation program. However, recent studies have shown that there are substantial differences in the sporulation programs between the two genera as well as among different Clostridium species. First, in the absence of a Bacillus-like phosphorelay system, activation of Spo0A in Clostridium organisms is carried out by a number of orphan histidine kinases. Second, downstream of Spo0A, the transcriptional and posttranslational regulation of the canonical set of four sporulation-specific sigma factors (σ(F), σ(E), σ(G), and σ(K)) display different patterns, not only compared to Bacillus but also among Clostridium organisms. Finally, recent studies demonstrated that σ(K), the last sigma factor to be activated according to the Bacillus subtilis model, is involved in the very early stages of sporulation in Clostridium acetobutylicum, C. perfringens, and C. botulinum as well as in the very late stages of spore maturation in C. acetobutylicum. Despite profound differences in initiation, propagation, and orchestration of expression of spore morphogenetic components, these findings demonstrate not only the robustness of the endospore sporulation program but also the plasticity of the program to generate different complex phenotypes, some apparently regulated at the epigenetic level.
Collapse
|
81
|
Elsayed OF, Maillard E, Vuilleumier S, Millet M, Imfeld G. Degradation of chloroacetanilide herbicides and bacterial community composition in lab-scale wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 520:222-231. [PMID: 25817759 DOI: 10.1016/j.scitotenv.2015.03.061] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 03/17/2015] [Accepted: 03/17/2015] [Indexed: 06/04/2023]
Abstract
Degradation of chloroacetanilide herbicides rac-metolachlor, acetochlor, and alachlor, as well as associated bacterial populations, were evaluated in vertical upflow wetland columns using a combination of hydrochemical and herbicide analyses, and DNA-based approaches. Mass dissipation of chloroacetanilides, continuously supplied at 1.8-1.9 μM for 112 days, mainly occurred in the rhizosphere zone under nitrate and sulphate-reducing conditions, and averaged 61±14%, 52±12% and 29±19% for acetochlor, alachlor and rac-metolachlor, respectively. Metolachlor enantiomer fractions of 0.494±0.009 in the oxic zone and 0.480±0.005 in the rhizosphere zone indicated preferential biodegradation of the S-enantiomer. Chloroacetanilide ethane sulfonic acid and oxanilic acid degradates were detected at low concentrations only (0.5 nM), suggesting extensive degradation and the operation of yet unknown pathways for chloroacetanilide degradation. Hydrochemical parameters and oxygen concentration were major drivers of bacterial composition, whereas exposure to chloroacetanilides had no detectable impact. Taken together, the results underline the importance of anaerobic degradation of chloroacetanilides in wetlands, and highlight the potential of complementary chemical and biological approaches to characterise processes involved in the environmental dissipation of chloroacetanilides.
Collapse
Affiliation(s)
- Omniea Fawzy Elsayed
- Laboratory of Hydrology and Geochemistry of Strasbourg (LHyGeS), University of Strasbourg/EOST, UMR 7517 CNRS, 1 rue Blessig, 67084 Strasbourg Cedex, France; Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, UMR 7156 CNRS, 28 rue Goethe, 67083 Strasbourg Cedex, France
| | - Elodie Maillard
- Laboratory of Hydrology and Geochemistry of Strasbourg (LHyGeS), University of Strasbourg/EOST, UMR 7517 CNRS, 1 rue Blessig, 67084 Strasbourg Cedex, France
| | - Stéphane Vuilleumier
- Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, UMR 7156 CNRS, 28 rue Goethe, 67083 Strasbourg Cedex, France
| | - Maurice Millet
- Institute of Chemistry for Energy, Environment and Health (ICPEES), University of Strasbourg, UMR 7515 CNRS, 1 rue Blessig, 67084 Strasbourg Cedex, France
| | - Gwenaël Imfeld
- Laboratory of Hydrology and Geochemistry of Strasbourg (LHyGeS), University of Strasbourg/EOST, UMR 7517 CNRS, 1 rue Blessig, 67084 Strasbourg Cedex, France.
| |
Collapse
|
82
|
Ramió-Pujol S, Ganigué R, Bañeras L, Colprim J. How can alcohol production be improved in carboxydotrophic clostridia? Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.03.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
83
|
Integrated, systems metabolic picture of acetone-butanol-ethanol fermentation by Clostridium acetobutylicum. Proc Natl Acad Sci U S A 2015; 112:8505-10. [PMID: 26100881 DOI: 10.1073/pnas.1423143112] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Microbial metabolism involves complex, system-level processes implemented via the orchestration of metabolic reactions, gene regulation, and environmental cues. One canonical example of such processes is acetone-butanol-ethanol (ABE) fermentation by Clostridium acetobutylicum, during which cells convert carbon sources to organic acids that are later reassimilated to produce solvents as a strategy for cellular survival. The complexity and systems nature of the process have been largely underappreciated, rendering challenges in understanding and optimizing solvent production. Here, we present a system-level computational framework for ABE fermentation that combines metabolic reactions, gene regulation, and environmental cues. We developed the framework by decomposing the entire system into three modules, building each module separately, and then assembling them back into an integrated system. During the model construction, a bottom-up approach was used to link molecular events at the single-cell level into the events at the population level. The integrated model was able to successfully reproduce ABE fermentations of the WT C. acetobutylicum (ATCC 824), as well as its mutants, using data obtained from our own experiments and from literature. Furthermore, the model confers successful predictions of the fermentations with various network perturbations across metabolic, genetic, and environmental aspects. From foundation to applications, the framework advances our understanding of complex clostridial metabolism and physiology and also facilitates the development of systems engineering strategies for the production of advanced biofuels.
Collapse
|
84
|
Cray JA, Stevenson A, Ball P, Bankar SB, Eleutherio ECA, Ezeji TC, Singhal RS, Thevelein JM, Timson DJ, Hallsworth JE. Chaotropicity: a key factor in product tolerance of biofuel-producing microorganisms. Curr Opin Biotechnol 2015; 33:228-59. [PMID: 25841213 DOI: 10.1016/j.copbio.2015.02.010] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/13/2015] [Accepted: 02/18/2015] [Indexed: 10/23/2022]
Abstract
Fermentation products can chaotropically disorder macromolecular systems and induce oxidative stress, thus inhibiting biofuel production. Recently, the chaotropic activities of ethanol, butanol and vanillin have been quantified (5.93, 37.4, 174kJ kg(-1)m(-1) respectively). Use of low temperatures and/or stabilizing (kosmotropic) substances, and other approaches, can reduce, neutralize or circumvent product-chaotropicity. However, there may be limits to the alcohol concentrations that cells can tolerate; e.g. for ethanol tolerance in the most robust Saccharomyces cerevisiae strains, these are close to both the solubility limit (<25%, w/v ethanol) and the water-activity limit of the most xerotolerant strains (0.880). Nevertheless, knowledge-based strategies to mitigate or neutralize chaotropicity could lead to major improvements in rates of product formation and yields, and also therefore in the economics of biofuel production.
Collapse
Affiliation(s)
- Jonathan A Cray
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - Andrew Stevenson
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - Philip Ball
- 18 Hillcourt Road, East Dulwich, London SE22 0PE, UK
| | - Sandip B Bankar
- Department of Chemical Engineering, College of Engineering, Bharati Vidyapeeth University, Pune-Satara Road, Pune 411043, India
| | - Elis C A Eleutherio
- Universidade Federal do Rio de Janeiro, Instituto de Quimica, Programa de Pós-graduação Bioquimica, Rio de Janeiro, RJ, Brazil
| | - Thaddeus C Ezeji
- Department of Animal Sciences and Ohio Agricultural Research and Development Center (OARDC), The Ohio State University, 305 Gerlaugh Hall, 1680 Madison Avenue, Wooster, OH 44691, USA
| | - Rekha S Singhal
- Department of Food Engineering and Technology, Institute of Chemical Technology, N.P. Marg, Matunga, Mumbai, Maharashtra 400019, India
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven and Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Flanders, Leuven-Heverlee B-3001, Belgium
| | - David J Timson
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland, UK.
| |
Collapse
|
85
|
Couchman EC, Browne HP, Dunn M, Lawley TD, Songer JG, Hall V, Petrovska L, Vidor C, Awad M, Lyras D, Fairweather NF. Clostridium sordellii genome analysis reveals plasmid localized toxin genes encoded within pathogenicity loci. BMC Genomics 2015; 16:392. [PMID: 25981746 PMCID: PMC4434542 DOI: 10.1186/s12864-015-1613-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 05/05/2015] [Indexed: 11/17/2022] Open
Abstract
Background Clostridium sordellii can cause severe infections in animals and humans, the latter associated with trauma, toxic shock and often-fatal gynaecological infections. Strains can produce two large clostridial cytotoxins (LCCs), TcsL and TcsH, related to those produced by Clostridium difficile, Clostridium novyi and Clostridium perfringens, but the genetic basis of toxin production remains uncharacterised. Results Phylogenetic analysis of the genome sequences of 44 strains isolated from human and animal infections in the UK, US and Australia placed the species into four clades. Although all strains originated from animal or clinical disease, only 5 strains contained LCC genes: 4 strains contain tcsL alone and one strain contains tcsL and tcsH. Four toxin-positive strains were found within one clade. Where present, tcsL and tcsH were localised in a pathogenicity locus, similar to but distinct from that present in C. difficile. In contrast to C. difficile, where the LCCs are chromosomally localised, the C. sordellii tcsL and tcsH genes are localised on plasmids. Our data suggest gain and loss of entire toxigenic plasmids in addition to horizontal transfer of the pathogenicity locus. A high quality, annotated sequence of ATCC9714 reveals many putative virulence factors including neuraminidase, phospholipase C and the cholesterol-dependent cytolysin sordellilysin that are highly conserved between all strains studied. Conclusions Genome analysis of C. sordellii reveals that the LCCs, the major virulence factors, are localised on plasmids. Many strains do not contain the LCC genes; it is probable that in several of these cases the plasmid has been lost upon laboratory subculture. Our data are consistent with LCCs being the primary virulence factors in the majority of infections, but LCC-negative strains may precipitate certain categories of infection. A high quality genome sequence reveals putative virulence factors whose role in virulence can be investigated. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1613-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Edward C Couchman
- Department of Life Sciences, Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK.
| | | | - Matt Dunn
- Wellcome Trust Sanger Institute, Hinxton, UK.
| | | | - J Glenn Songer
- Department of Veterinary Science and Microbiology, University of Arizona, Tucson, USA.
| | - Val Hall
- Anaerobe Reference Laboratory, University Hospital of Wales, Cardiff, UK.
| | | | - Callum Vidor
- Department of Microbiology, Monash University, Clayton, VIC, 3800, Australia.
| | - Milena Awad
- Department of Microbiology, Monash University, Clayton, VIC, 3800, Australia.
| | - Dena Lyras
- Department of Microbiology, Monash University, Clayton, VIC, 3800, Australia.
| | - Neil F Fairweather
- Department of Life Sciences, Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK.
| |
Collapse
|
86
|
Xiao Y, van Hijum SAFT, Abee T, Wells-Bennik MHJ. Genome-Wide Transcriptional Profiling of Clostridium perfringens SM101 during Sporulation Extends the Core of Putative Sporulation Genes and Genes Determining Spore Properties and Germination Characteristics. PLoS One 2015; 10:e0127036. [PMID: 25978838 PMCID: PMC4433262 DOI: 10.1371/journal.pone.0127036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 04/11/2015] [Indexed: 11/19/2022] Open
Abstract
The formation of bacterial spores is a highly regulated process and the ultimate properties of the spores are determined during sporulation and subsequent maturation. A wide variety of genes that are expressed during sporulation determine spore properties such as resistance to heat and other adverse environmental conditions, dormancy and germination responses. In this study we characterized the sporulation phases of C. perfringens enterotoxic strain SM101 based on morphological characteristics, biomass accumulation (OD600), the total viable counts of cells plus spores, the viable count of heat resistant spores alone, the pH of the supernatant, enterotoxin production and dipicolinic acid accumulation. Subsequently, whole-genome expression profiling during key phases of the sporulation process was performed using DNA microarrays, and genes were clustered based on their time-course expression profiles during sporulation. The majority of previously characterized C. perfringens germination genes showed upregulated expression profiles in time during sporulation and belonged to two main clusters of genes. These clusters with up-regulated genes contained a large number of C. perfringens genes which are homologs of Bacillus genes with roles in sporulation and germination; this study therefore suggests that those homologs are functional in C. perfringens. A comprehensive homology search revealed that approximately half of the upregulated genes in the two clusters are conserved within a broad range of sporeforming Firmicutes. Another 30% of upregulated genes in the two clusters were found only in Clostridium species, while the remaining 20% appeared to be specific for C. perfringens. These newly identified genes may add to the repertoire of genes with roles in sporulation and determining spore properties including germination behavior. Their exact roles remain to be elucidated in future studies.
Collapse
Affiliation(s)
- Yinghua Xiao
- NIZO food research, Ede, The Netherlands
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Laboratory of Food Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Sacha A. F. T. van Hijum
- NIZO food research, Ede, The Netherlands
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tjakko Abee
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Laboratory of Food Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Marjon H. J. Wells-Bennik
- NIZO food research, Ede, The Netherlands
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- * E-mail:
| |
Collapse
|
87
|
Updates on the sporulation process in Clostridium species. Res Microbiol 2015; 166:225-35. [DOI: 10.1016/j.resmic.2014.12.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 12/07/2014] [Accepted: 12/09/2014] [Indexed: 12/19/2022]
|
88
|
Weighill DA, Jacobson DA. 3-way networks: application of hypergraphs for modelling increased complexity in comparative genomics. PLoS Comput Biol 2015; 11:e1004079. [PMID: 25815802 PMCID: PMC4376783 DOI: 10.1371/journal.pcbi.1004079] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 12/08/2014] [Indexed: 11/24/2022] Open
Abstract
We present and develop the theory of 3-way networks, a type of hypergraph in which each edge models relationships between triplets of objects as opposed to pairs of objects as done by standard network models. We explore approaches of how to prune these 3-way networks, illustrate their utility in comparative genomics and demonstrate how they find relationships which would be missed by standard 2-way network models using a phylogenomic dataset of 211 bacterial genomes. Genomes contain the information underlying the molecular functions of an organism. One way to compare the entire genomes of different organisms is to compare their gene-family content profiles which is effectively a comparison of their functional potential. Standard networks, when used to model phylogenomic similarities, are not capable of capturing some of the underlying complexity of the relationships between genomes. In order to address this, we have developed a new three-way similarity metric and constructed three-way networks modelling the relationships between 211 bacterial genomes. We find that such three-way networks find cross-species genomic similarities that would have been otherwise missed by simpler models such as standard networks.
Collapse
Affiliation(s)
- Deborah A Weighill
- Institute for Wine Biotechnology, Stellenbosch University, Stellenbosch, South Africa
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Daniel A Jacobson
- Institute for Wine Biotechnology, Stellenbosch University, Stellenbosch, South Africa
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- * E-mail:
| |
Collapse
|
89
|
Phylogenetic and functional alterations in bacterial community compositions in broiler ceca as a result of mannan oligosaccharide supplementation. Appl Environ Microbiol 2015; 81:3460-70. [PMID: 25769823 DOI: 10.1128/aem.04194-14] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 03/05/2015] [Indexed: 12/20/2022] Open
Abstract
This study focused on identifying reproducible effects of dietary supplementation with a mannan oligosaccharide (MOS) on the broiler cecal bacterial community structure and function in a commercial production setting. Two separate trials, each with a control and a supplemented group, were carried out in the same commercial location and run concurrently. Approximately 10,000 birds from the same commercial hatchery were mirror imaged into each of four commercial broiler sheds and fed either a control or supplemented diet. Cecal contents were obtained on days 7, 21, and 35 posthatch from 12 randomly caught broilers from each group. Bacterial pyrosequencing was performed on all samples, with approximately 250,000 sequences obtained per treatment per time point. The predominant phyla identified at all three time points in both trials were Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Tenericutes, representing >99% of all sequences. MOS supplementation altered the bacterial community composition from 7 days supplementation through 35 days supplementation. Bacteroidetes appeared to be replacing Firmicutes as a result of supplementation, with the most noticeable effects after 35 days. The effects of supplementation were reproducible across both trials. PICRUSt was used to identify differences between the functional potentials of the bacterial communities as a result of MOS supplementation. Using level 3 KEGG ortholog function predictions, differences between control and supplemented groups were observed, with very strong segregation noted on day 35 posthatch in both trials. This indicated that alterations of bacterial communities as a result of MOS are likely to alter the functional capability of the cecum.
Collapse
|
90
|
Abstract
Clostridium difficile is the most common cause of antibiotic-associated intestinal infections and a significant cause of morbidity and mortality. Infection with C. difficile requires disruption of the intestinal microbiota, most commonly by antibiotic usage. Therapeutic intervention largely relies on a small number of broad-spectrum antibiotics, which further exacerbate intestinal dysbiosis and leave the patient acutely sensitive to reinfection. Development of novel targeted therapeutic interventions will require a detailed knowledge of essential cellular processes, which represent attractive targets, and species-specific processes, such as bacterial sporulation. Our knowledge of the genetic basis of C. difficile infection has been hampered by a lack of genetic tools, although recent developments have made some headway in addressing this limitation. Here we describe the development of a method for rapidly generating large numbers of transposon mutants in clinically important strains of C. difficile. We validated our transposon mutagenesis approach in a model strain of C. difficile and then generated a comprehensive transposon library in the highly virulent epidemic strain R20291 (027/BI/NAP1) containing more than 70,000 unique mutants. Using transposon-directed insertion site sequencing (TraDIS), we have identified a core set of 404 essential genes, required for growth in vitro. We then applied this technique to the process of sporulation, an absolute requirement for C. difficile transmission and pathogenesis, identifying 798 genes that are likely to impact spore production. The data generated in this study will form a valuable resource for the community and inform future research on this important human pathogen. Clostridium difficile is a common cause of potentially fatal intestinal infections in hospital patients, particularly those who have been treated with antibiotics. Our knowledge of this bacterium has been hampered by a lack of tools for dissecting the organism. We have developed a method to study the function of every gene in the bacterium simultaneously. Using this tool, we have identified a set of 404 genes that are required for growth of the bacteria in the laboratory. C. difficile also produces a highly resistant spore that can survive in the environment for a long time and is a requirement for transmission of the bacteria between patients. We have applied our genetic tool to identify all of the genes required for production of a spore. All of these genes represent attractive targets for new drugs to treat infection.
Collapse
|
91
|
Abstract
We report here the closed genome of Clostridium pasteurianum ATCC 6013, a saccharolytic, nitrogen-fixing, and spore-forming Gram-positive obligate anaerobe. The organism is of biotechnological interest due to the production of solvents (butanol and 1,3-propanediol) but can be associated with food spoilage. The genome comprises a total of 4,351,223 bp.
Collapse
|
92
|
Fimlaid KA, Shen A. Diverse mechanisms regulate sporulation sigma factor activity in the Firmicutes. Curr Opin Microbiol 2015; 24:88-95. [PMID: 25646759 DOI: 10.1016/j.mib.2015.01.006] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/23/2014] [Accepted: 01/10/2015] [Indexed: 11/27/2022]
Abstract
Sporulation allows bacteria to survive adverse conditions and is essential to the lifecycle of some obligate anaerobes. In Bacillus subtilis, the sporulation-specific sigma factors, σ(F), σ(E), σ(G), and σ(K), activate compartment-specific transcriptional programs that drive sporulation through its morphological stages. The regulation of these sigma factors was predicted to be conserved across the Firmicutes, since the regulatory proteins controlling their activation are largely conserved. However, recent studies in (Pepto)Clostridium difficile, Clostridium acetobutylicum, Clostridium perfringens, and Clostridium botulinum have revealed striking differences in the order, activation, and function of sporulation sigma factors. These studies indicate that gene conservation does not necessarily predict gene function and that new mechanisms for controlling cell fate determination remain to be discovered in the anaerobic Clostridia.
Collapse
Affiliation(s)
- Kelly A Fimlaid
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; Cellular, Molecular and Biomedical Sciences Program, University of Vermont, Burlington, VT 05405, USA
| | - Aimee Shen
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA.
| |
Collapse
|
93
|
Hosomi K, Kuwana R, Takamatsu H, Kohda T, Kozaki S, Mukamoto M. Morphological and genetic characterization of group I Clostridium botulinum type B strain 111 and the transcriptional regulator spoIIID gene knockout mutant in sporulation. Anaerobe 2015; 33:55-63. [PMID: 25652599 DOI: 10.1016/j.anaerobe.2015.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/29/2015] [Accepted: 01/30/2015] [Indexed: 11/26/2022]
Abstract
Clostridium botulinum is a heat-resistant spore-forming bacterium that causes the serious paralytic illness botulism. Heat-resistant spores may cause food sanitation hazards and sporulation plays a central role in the survival of C. botulinum. We observed morphological changes and investigated the role of the transcriptional regulator SpoIIID in the sporulation of C. botulinum type B strain 111 in order to elucidate the molecular mechanism in C. botulinum. C. botulinum type B formed heat-resistant spores through successive morphological changes corresponding to those of Bacillus subtilis, a spore-forming model organism. An analysis of the spoIIID gene knockout mutant revealed that the transcriptional regulator SpoIIID contributed to heat-resistant spore formation by C. botulinum type B and activated the transcription of the sigK gene later during sporulation. Transcription of the spoIIID gene, which differed from that in B. subtilis and Clostridium difficile, was observed in the sigE gene knockout mutant of C. botulinum type B. An analysis of the sigF gene knockout mutant showed that the sporulation-specific sigma factor SigF was essential for transcription of the spoIIID gene in C. botulinum type B. These results suggest that the regulation of sporulation in C. botulinum is not similar to that in B. subtilis and other clostridia.
Collapse
Affiliation(s)
- Koji Hosomi
- Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Ritsuko Kuwana
- Faculty of Pharmaceutical Sciences, Setsunan University, Hirakata, Osaka, Japan
| | - Hiromu Takamatsu
- Faculty of Pharmaceutical Sciences, Setsunan University, Hirakata, Osaka, Japan
| | - Tomoko Kohda
- Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Shunji Kozaki
- Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Masafumi Mukamoto
- Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan.
| |
Collapse
|
94
|
Köhler KAK, Rühl J, Blank LM, Schmid A. Integration of biocatalyst and process engineering for sustainable and efficientn-butanol production. Eng Life Sci 2015. [DOI: 10.1002/elsc.201400041] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
| | - Jana Rühl
- Laboratory of Chemical Biotechnology; TU Dortmund University; Dortmund Germany
| | - Lars M. Blank
- Institute of Applied Microbiology (iAMB); Aachen Biology and Biotechnology (ABBt); RWTH Aachen University; Aachen Germany
| | - Andreas Schmid
- Department Solar Materials; Helmholtz Centre for Environmental Research (UFZ); Leipzig Germany
| |
Collapse
|
95
|
Tan Y, Liu ZY, Liu Z, Zheng HJ, Li FL. Comparative transcriptome analysis between csrA-disruption Clostridium acetobutylicum and its parent strain. MOLECULAR BIOSYSTEMS 2015; 11:1434-42. [DOI: 10.1039/c4mb00600c] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This study represented the first attempt to investigate the global regulation of CsrA through transcriptome analysis in Gram-positive bacteria.
Collapse
Affiliation(s)
- Yang Tan
- Key Laboratory of Biofuels
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- China
| | - Zi-Yong Liu
- Key Laboratory of Biofuels
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- China
| | - Zhen Liu
- Key Laboratory of Biofuels
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- China
| | - Hua-Jun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics
- Chinese National Human Genome Center at Shanghai
- Shanghai 201203
- China
| | - Fu-Li Li
- Key Laboratory of Biofuels
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- China
| |
Collapse
|
96
|
Abstract
Since the first application of high hydrostatic pressure (HHP) for food preservation more than 100 years ago, a wealth of knowledge has been gained on molecular mechanisms underlying the HHP-mediated destruction of microorganisms. However, one observation made back then is still valid, i.e. that HHP alone is not sufficient for the complete inactivation of bacterial endospores. To achieve "commercial sterility" of low-acid foods, i.e. inactivation of spores capable of growing in a specific product under typical storage conditions, a combination of HHP with other hurdles is required (most effectively with heat (HPT)). Although HPT processes are not yet industrially applied, continuous technical progress and increasing consumer demand for minimally processed, additive-free food with long shelf life, makes HPT sterilization a promising alternative to thermal processing.In recent years, considerable progress has been made in understanding the response of spores of the model organism B. subtilis to HPT treatments and detailed insights into some basic mechanisms in Clostridium species shed new light on differences in the HPT-mediated inactivation of Bacillus and Clostridium spores. In this chapter, current knowledge on sporulation and germination processes, which presents the basis for understanding development and loss of the extreme resistance properties of spores, is summarized highlighting commonalities and differences between Bacillus and Clostridium species. In this context, the effect of HPT treatments on spores, inactivation mechanism and kinetics, the role of population heterogeneity, and influence factors on the results of inactivation studies are discussed.
Collapse
Affiliation(s)
- Christian A Lenz
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, 85354, Freising, Germany
| | | |
Collapse
|
97
|
Sandoval NR, Venkataramanan KP, Groth TS, Papoutsakis ET. Whole-genome sequence of an evolved Clostridium pasteurianum strain reveals Spo0A deficiency responsible for increased butanol production and superior growth. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:227. [PMID: 26705421 PMCID: PMC4690370 DOI: 10.1186/s13068-015-0408-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/03/2015] [Indexed: 05/23/2023]
Abstract
BACKGROUND Biodiesel production results in crude glycerol waste from the transesterification of fatty acids (10 % w/w). The solventogenic Clostridium pasteurianum, an anaerobic Firmicute, can produce butanol from glycerol as the sole carbon source. Coupling butanol fermentation with biodiesel production can improve the overall economic viability of biofuels. However, crude glycerol contains growth-inhibiting byproducts which reduce feedstock consumption and solvent production. RESULTS To obtain a strain with improved characteristics, a random mutagenesis and directed evolution selection technique was used. A wild-type C. pasteurianum (ATCC 6013) culture was chemically mutagenized, and the resulting population underwent 10 days of selection in increasing concentrations of crude glycerol (80-150 g/L). The best-performing mutant (M150B) showed a 91 % increase in butanol production in 100 g/L crude glycerol compared to the wild-type strain, as well as increased growth rate, a higher final optical density, and less production of the side product PDO (1,3-propanediol). Wild-type and M150B strains were sequenced via Single Molecule Real-Time (SMRT) sequencing. Mutations introduced to the M150B genome were identified by sequence comparison to the wild-type and published closed sequences. A major mutation (a deletion) in the gene of the master transcriptional regulator of sporulation, Spo0A, was identified. A spo0A single gene knockout strain was constructed using a double--crossover genome-editing method. The Spo0A-deficient strain showed similar tolerance to crude glycerol as the evolved mutant strain M150B. Methylation patterns on genomic DNA identified by SMRT sequencing were used to transform plasmid DNA to overcome the native C. pasteurianum restriction endonuclease. CONCLUSIONS Solvent production in the absence of Spo0A shows C. pasteurianum differs in solvent-production regulation compared to other solventogenic Clostridium. Growth-associated butanol production shows C. pasteurianum to be an attractive option for further engineering as it may prove a better candidate for butanol production through continuous fermentation.
Collapse
Affiliation(s)
- Nicholas R. Sandoval
- />Department of Chemical and Biomolecular Engineering and the Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711 USA
| | - Keerthi P. Venkataramanan
- />Department of Chemical and Biomolecular Engineering and the Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711 USA
| | - Theodore S. Groth
- />Department of Chemical and Biomolecular Engineering and the Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711 USA
| | - Eleftherios T. Papoutsakis
- />Department of Chemical and Biomolecular Engineering and the Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711 USA
- />Department of Biological Sciences, University of Delaware, Newark, USA
| |
Collapse
|
98
|
Tao W, Dong H, Zhang Y, Cai Z, Li Y. Introducing transglutaminase with its precursor region into Clostridium acetobutylicum improves its tolerance to oxidative stress and solvent production. Process Biochem 2015. [DOI: 10.1016/j.procbio.2014.10.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
99
|
Peng XING, Wangting HU, Yufan WU, Qinglong WU. Major progress in microbial ecology of hypoxia in the shallow eutrophic lakes. ACTA ACUST UNITED AC 2015. [DOI: 10.18307/2015.0402] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
|
100
|
Engineering Clostridium acetobutylicum with a histidine kinase knockout for enhanced n-butanol tolerance and production. Appl Microbiol Biotechnol 2014; 99:1011-22. [DOI: 10.1007/s00253-014-6249-7] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 11/17/2014] [Accepted: 11/18/2014] [Indexed: 01/07/2023]
|